Datasetpublic

LiteFold/PDB-CCD

PDB Chemical Component Dictionary PDB-CCD is the Chemical Component Dictionary used by the Protein Data Bank to describe residues, modified residues, ligands, solvents, and other chemical components in macromolecular structures. Splits The split is deterministic by component identifier: sha256(component_id) % 10. Bucket 0 is test; buckets 1 through 9 are train. Split Rows train 45,045 test 5,009 total 50,054 Dataset Statistics… See the full description on the dataset page: https://huggingface.co/datasets/LiteFold/PDB-CCD.

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PDB Chemical Component Dictionary

PDB-CCD is the Chemical Component Dictionary used by the Protein Data Bank to describe residues, modified residues, ligands, solvents, and other chemical components in macromolecular structures.

Splits

The split is deterministic by component identifier: sha256(component_id) % 10. Bucket 0 is test; buckets 1 through 9 are train.

Split	Rows
train	45,045
test	5,009
total	50,054

Dataset Statistics

Field	Value
Components	50,054
Released components	49,292
Obsolete components	762
Components with atoms	49,947
Components with bonds	49,921
Components with descriptors	50,052
Components with identifiers	37,058
Components with PCM annotations	613
Latest modified date in source	`2026-04-24`

Common component type	Rows
NON-POLYMER	26,117
non-polymer	19,493
L-PEPTIDE LINKING	923
L-peptide linking	580
peptide-like	556
D-saccharide	405
DNA LINKING	325
RNA LINKING	223

Usage

Install the Hugging Face Datasets library:

bash

pip install datasets

Load all splits:

python

from datasets import load_dataset

ds = load_dataset("LiteFold/PDB-CCD")
print(ds)

row = ds["train"][0]
print(row["component_id"], row["name"], row["formula"])

Load one split:

python

from datasets import load_dataset

train = load_dataset("LiteFold/PDB-CCD", split="train")
test = load_dataset("LiteFold/PDB-CCD", split="test")

Stream rows without downloading the full table first:

python

from datasets import load_dataset

stream = load_dataset("LiteFold/PDB-CCD", split="train", streaming=True)
for row in stream.take(5):
    print(row["component_id"], row["canonical_smiles"], row["atom_count"])

Filter released non-polymer components with InChIKeys:

python

from datasets import load_dataset

ds = load_dataset("LiteFold/PDB-CCD", split="train")
released = ds.filter(
    lambda row: row["release_status"] == "REL"
    and row["component_type"] in {"NON-POLYMER", "non-polymer"}
    and row["inchikey"] is not None
)
print(released[0])

Find components modified after a date:

python

from datasets import load_dataset

ds = load_dataset("LiteFold/PDB-CCD", split="train")
recent = ds.filter(lambda row: row["modified_date"] is not None and row["modified_date"] >= "2026-01-01")
print(recent[0]["component_id"], recent[0]["modified_date"])

Columns

Column	Description
`component_id`	Chemical component identifier.
`name`	Component name from `_chem_comp.name`.
`component_type`	Raw `_chem_comp.type` value.
`pdbx_type`	Raw `_chem_comp.pdbx_type` value.
`formula`	Chemical formula.
`formula_weight`	Formula weight as a float.
`formal_charge`	Formal charge as an integer.
`mon_nstd_parent_comp_id`	Parent component ID for non-standard monomers, when present.
`one_letter_code`	One-letter code, when present.
`three_letter_code`	Three-letter code, when present.
`pdbx_synonyms`	Synonym field from `_chem_comp`.
`synonym_names`	Synonyms from `pdbx_chem_comp_synonyms`.
`initial_date`	Initial component date.
`modified_date`	Last modified date.
`release_status`	Release status, such as `REL` or `OBS`.
`replaced_by`	Replacement component ID, when present.
`replaces`	Component ID replaced by this component, when present.
`atom_ids`	Atom identifiers from `chem_comp_atom`.
`atom_elements`	Element symbols for `atom_ids`.
`atom_charges`	Atom charges.
`atom_aromatic_flags`	Atom aromatic flags.
`atom_leaving_flags`	Atom leaving-atom flags.
`atom_stereo_configs`	Atom stereochemistry flags.
`atom_count`	Number of atoms.
`heavy_atom_count`	Number of non-hydrogen atoms.
`hydrogen_atom_count`	Number of hydrogen atoms.
`bond_atom_id_1`	First atom ID for each bond.
`bond_atom_id_2`	Second atom ID for each bond.
`bond_orders`	Bond order values.
`bond_aromatic_flags`	Bond aromatic flags.
`bond_stereo_configs`	Bond stereochemistry flags.
`bond_count`	Number of bonds.
`descriptor_types`	Descriptor types such as `SMILES`, `SMILES_CANONICAL`, `InChI`, and `InChIKey`.
`descriptors`	Descriptor values.
`canonical_smiles`	First `SMILES_CANONICAL` descriptor.
`smiles`	First `SMILES` descriptor.
`inchi`	First `InChI` descriptor.
`inchikey`	First `InChIKey` descriptor.
`identifier_types`	Identifier types from `pdbx_chem_comp_identifier`.
`identifiers`	Identifier values.
`systematic_names`	Identifier values whose type is `SYSTEMATIC NAME`.
`audit_actions`	Audit action types.
`audit_dates`	Audit dates.
`related_component_ids`	Related component IDs, when present.
`pcm_ids`	Protein modification annotation IDs, when present.
`pcm_modified_residue_ids`	Modified residue IDs from PCM annotations.
`feature_types`	Feature types from `pdbx_chem_comp_feature`.
`feature_values`	Feature values from `pdbx_chem_comp_feature`.
`split_bucket`	Deterministic split bucket from `sha256(component_id) % 10`.

Citation

@article{westbrook2015pdbccd,
  title   = {The chemical component dictionary: complete descriptions of constituent molecules in experimentally determined 3D macromolecules in the Protein Data Bank},
  author  = {Westbrook, John D. and Shao, Chuming and Feng, Zukang and Zhuravleva, Maria and Velankar, Sameer and Young, Jasmine},
  journal = {Bioinformatics},
  volume  = {31},
  number  = {8},
  pages   = {1274--1278},
  year    = {2015},
  doi     = {10.1093/bioinformatics/btu789}
}